Friday's brief statement by the independent commission said the unspecified problems had "affected the sound level in the debate hall".
Representatives for the Commission didn't immediately respond Friday afternoon to a request for details about the audio problems.
Trump complained to reporters after the debate that his microphone was defective, according to CNN.
The Commission on Presidential Debate's is a non-profit corporation that is sponsored by several Fortune 500 companies and was formed in 1987 by leadership of American's two largest political parties.
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Republican presidential nominee Donald Trump (L) speaks as Democratic presidential nominee Hillary Clinton listens on during the Presidential Debate at Hofstra University on September 26, 2016 in Hempstead, New York. I wonder was it set up that way on objective - my microphone, in the room, they couldn't hear me.
"My microphone in the room, they couldn't hear me", Trump said on Fox and Friends. Of course, Trump must have been complaining about the mic as an excuse for "losing the debate" to Hillary Clinton. "When I tested it before, it was attractive".
Officials did not provide any evidence that showed the audio affected the TV experience of the debate for the 80 million viewers watching at home.
Trump has pitched his stamina as an important qualification for the White House, drawing a contrast with Clinton, whose health scare left her unable to stand up on her own at a public event on September 11.
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The New Yorker said he was open to changing the law but not in any way that could hurt the 9/11 families, many of whom are his constituents.